A supervised learning framework for pancreatic islet segmentation with multi-scale color-texture features and rolling guidance filters.

Islet cell quantification and function is important for developing novel therapeutic interventions for diabetes. Existing methods of pancreatic islet segmentation in histopathological images depend strongly on cell/nuclei detection, and thus are limited due to a wide variance in the appearance of pancreatic islets. In this paper, we propose a supervised learning pipeline to segment pancreatic islets in histopathological images, which does not require cell detection. The proposed framework firstly partitions images into superpixels, and then extracts multi-scale color-texture features from each superpixel and processes these features using rolling guidance filters, in order to simultaneously reduce inter-class ambiguity and intra-class variation. Finally, a linear support vector machine (SVM) is trained and applied to segment the testing images. A total of 23 hematoxylin-and-eosin-stained histopathological images with pancreatic islets are used for verifying the framework. With an average accuracy of 95%, training time of 20 min and testing time of 1 min per image, the proposed framework outperforms existing approaches with better segmentation performance and lower computational cost. © 2016 International Society for Advancement of Cytometry.

Breast Tumor Tissue Segmentation with Area-Based Annotation Using Convolutional Neural Network.

In this paper, we propose a novel approach to segment tumor and normal regions in human breast tissues. Cancer is the second most common cause of death in our society; every eighth woman will be diagnosed with breast cancer in her life. Histological diagnosis is key in the process where oncotherapy is administered. Due to the time-consuming analysis and the lack of specialists alike, obtaining a timely diagnosis is often a difficult process in healthcare institutions, so there is an urgent need for improvement in diagnostics. To reduce costs and speed up the process, an automated algorithm could aid routine diagnostics. We propose an area-based annotation approach generalized by a new rule template to accurately solve high-resolution biological segmentation tasks in a time-efficient way. These algorithm and implementation rules provide an alternative solution for pathologists to make decisions as accurate as manually. This research is based on an individual database from Semmelweis University, containing 291 high-resolution, bright field microscopy breast tumor tissue images. A total of 70% of the 128 × 128-pixel resolution images (206,174 patches) were used for training a convolutional neural network to learn the features of normal and tumor tissue samples. The evaluation of the small regions results in high-resolution histopathological image segmentation; the optimal parameters were calculated on the validation dataset (29 images, 10%), considering the accuracy and time factor as well. The algorithm was tested on the test dataset (61 images, 20%), reaching a 99.10% f1 score on pixel level evaluation within 3 min on average. Besides the quantitative analyses, the system's accuracy was measured qualitatively by a histopathologist, who confirmed that the algorithm was also accurate in regions not annotated before.

An EM-based semi-supervised deep learning approach for semantic segmentation of histopathological images from radical prostatectomies.

Automated Gleason grading is an important preliminary step for quantitative histopathological feature extraction. Different from the traditional task of classifying small pre-selected homogeneous regions, semantic segmentation provides pixel-wise Gleason predictions across an entire slide. Deep learning-based segmentation models can automatically learn visual semantics from data, which alleviates the need for feature engineering. However, performance of deep learning models is limited by the scarcity of large-scale fully annotated datasets, which can be both expensive and time-consuming to create. One way to address this problem is to leverage external weakly labeled datasets to augment models trained on the limited data. In this paper, we developed an expectation maximization-based approach constrained by an approximated prior distribution in order to extract useful representations from a large number of weakly labeled images generated from low-magnification annotations. This method was utilized to improve the performance of a model trained on a limited fully annotated dataset. Our semi-supervised approach trained with 135 fully annotated and 1800 weakly annotated tiles achieved a mean Jaccard Index of 49.5% on an independent test set, which was 14% higher than the initial model trained only on the fully annotated dataset.